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2.5 years ago this was my daily driver, lovely car sweet as anything. I put the car in for its annual MOT (ministry safety) test and it failed for emissions. I picked the car up and could barely drive the thing home. One of the exhuast valves was burnt out. I am to this day dubious that it should happen on the emissions test as the car is tested at idle and fast idle only. Live and let live though.

Car is now rebuilt - 2.5years later . It has been standing for a long time without a battery. Whilst the heads were off I ported them and raised the comp a little. Fitted a new lambda sensor and obviously - a new battery. The car passed its emissions test. These last two paragraphs may well be irrelevant.....

I have done about 6 journeys subsequent to its rebuild. Varying from 2 miles to 150miles. About 4 times during these journeys the CEL has lit - for no more than 30seconds - and knocked a lot of torque out of the engine (feels like max ign retard). The only common occurance is that it tends to trigger at lower vehicle speeds - say below 30mph.

Because I have a JECS ECU the OBD is of little use to me as it is not OBD2 compliant (EU didn't have to be compliant until 2003 for petrol cars). I seem to remember that I can short the connectors between the steering column to read the flashes off the CEL. However, I don't have a perm CEL, only intermittant, will I still be shown the true fault path without a perm fault code?

Any answers regarding what may be wrong are purely speculative until you are able to read the code. If it's not an OBDII code you may have to do some searching for info on it (once you have the actual code), and you will probably find more info on another board such as Scoobynet where they are familiar with your model.
In the US our OBDII transition year was '96. You might try the info here to retrieve the code, whether or not there is any code stored will be answered at that point assuming the check procedure works-http://www.troublecodes.net/Subaru/
If the fuel is really that old you may want to drain the tank or at least remove a sample from the bottom and check for water or crud. If you find any, drain the tank completely and flush the lines. That may or may not have anything to do with the light/codes but it's still a good idea for a car that has been sitting with fuel in it.